8TQ8: Fab.34.5.8

Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd). Determined by X-ray diffraction at 2.69 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 10
Atoms: 12,558
Mol. weight: 184.91 kDa
Released: 20 Mar 2024

Explore 8TQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TQ8 contains 41 α-helices and 145 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-224	3	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chains B and D: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-56	7	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	19
α-helix	184-185	2
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	213-219	7	21
β-strand	222-223	2	21
β-strand	229-230	2	20
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	253-255	3
β-strand	257-263	7	21
β-strand	270-272	3	21

Chain F: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	25
β-strand	10-11	2	26
β-strand	17-23	7	25
α-helix	29-31	3
β-strand	34-39	6	27
β-strand	45-52	8	27
β-strand	57-60	4	27
β-strand	65	1	25
β-strand	68-73	6	25
β-strand	78-84	7	25
β-strand	93-99	7	27
β-strand	106-109	4	27
β-strand	113-114	2	27
β-strand	115-116	2	26
β-strand	126-130	5	28
β-strand	143-151	9	28
β-strand	157-160	4	29
β-strand	170-171	2	28
α-helix	173-174	2
β-strand	175-177	3	28
β-strand	180-188	9	28
α-helix	193-196	4
β-strand	201-205	5	29
β-strand	210-214	5	29

Chain G: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	30
β-strand	10-12	3	31
β-strand	19-24	6	30
β-strand	31	1	32
β-strand	34	1	32
β-strand	37-42	6	31
β-strand	49-53	5	31
β-strand	57-58	2	31
α-helix	59	1
β-strand	67-71	5	30
β-strand	74-79	6	30
β-strand	89-94	6	31
β-strand	102-103	2	31
β-strand	107-110	4	31
β-strand	116	1	33
β-strand	119-123	5	34
α-helix	127-132	6
β-strand	134-144	11	34
β-strand	145	1	33
β-strand	150-155	6	35
β-strand	158-160	3	35
β-strand	164-168	5	34
α-helix	170-172	3
β-strand	178-187	10	34
α-helix	188-192	5
β-strand	198-203	6	35
β-strand	206-213	8	35

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	8
β-strand	10-12	3	9
β-strand	17-23	7	8
α-helix	29-31	3
β-strand	34-39	6	9
α-helix	40	1
β-strand	45-52	8	9
β-strand	57-60	4	9
α-helix	62-64	3
β-strand	65	1	8
β-strand	68-73	6	8
α-helix	74-76	3
β-strand	78-84	7	8
β-strand	92-99	8	9
β-strand	106-109	4	9
β-strand	113-117	5	9
β-strand	126-129	4	10
β-strand	142-143	2	11
β-strand	146-149	4	10
β-strand	157-160	4	12
β-strand	169-171	3	10
α-helix	173-174	2
β-strand	175-177	3	10
β-strand	180-187	8	10
β-strand	188-189	2	11
β-strand	200-205	6	12
β-strand	210-215	6	12

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-12	3	14
β-strand	19-25	7	13
β-strand	37-42	6	14
β-strand	49-53	5	14
β-strand	57-58	2	14
α-helix	59	1
β-strand	66-71	6	13
β-strand	74-79	6	13
β-strand	89-94	6	14
β-strand	102-103	2	14
β-strand	107-110	4	14
β-strand	116	1	15
β-strand	119-123	5	16
α-helix	127-131	5
β-strand	134-144	11	16
β-strand	145	1	15
β-strand	150-155	6	17
β-strand	158-160	3	17
β-strand	164-168	5	16
α-helix	170-172	3
β-strand	178-187	10	16
α-helix	188-192	5
β-strand	198-202	5	17
β-strand	210-213	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, C	protein	273	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	99	Mus musculus	P01887 (AlphaFold model)
Transmembrane protein gp41	E, P	protein	10	Human immunodeficiency virus 1	P04578 (AlphaFold model)
Fab.34.5.8 Heavy chain	F, H	protein	219	Mus musculus
Fab.34.5.8 Light chain	G, L	protein	219	Mus musculus

Sequence of entity 1 (A, C), FASTA

>8TQ8_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, C)
SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWE
RETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGC
DYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLR
TDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTF
QKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW

Sequence of entity 2 (B, D), FASTA

>8TQ8_2 Beta-2-microglobulin (chains B, D)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (E, P), FASTA

>8TQ8_3 Transmembrane protein gp41 (chains E, P)
RGPGRAFVTI

Sequence of entity 4 (F, H), FASTA

>8TQ8_4 Fab.34.5.8 Heavy chain (chains F, H)
SVQLEESGPELGKPGASVKMSCTASGYAFTSYVMHWVMQKPGQGLEWIGYFNPYNDGAKY
NAKFKGKATLTSDKSSNTAYMELSSLTSEDSTVYYCARAYFSKGPFAYWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPV

Sequence of entity 5 (G, L), FASTA

>8TQ8_5 Fab.34.5.8 Light chain (chains G, L)
LISMTQTPASLAVSLGQRATISCRASESVDRHGNSFMHWYQQKPGQPPKLLIYRASNLDS
GIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPPWTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. Boyd, L.F., Jiang, J., Ahmad, J. et al. J Immunol (2024) 212:1366-1380. DOI 10.4049/jimmunol.2300839 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…

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